Team:EPF Lausanne

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BioPad

EPFL

Introduction

Most sciences have the advantage of being able to detect and process signals in a fast and efficient way. Biology lacks this ability as signal detection and processing requires large amounts of time leading to inaccuracies and potential interferences from external sources. We aim to improve this and make signal induction faster and more accurate while designing an innovating new biological machine using protein complementation techniques.

As a proof of concept of this new way of viewing biology, this year’s EPFL iGEM team aims to build the first biological touchpad, hereafter referred as the BioPad, allowing users to control electronics in real time through living organisms.

On top of its potential use a touchpad, the BioPad will have several applications: deliver a cheap, fast, efficient, and accurate antibiotic screening system; as well as providing a new way for studying genes by allowing the study of the the relationship between genes and their corresponding activating signals.

The Bio Pad

Our biological Touch Pad will allow the control of electronic by emitting light at the specific location where the Pad has been touched. Light emission is possible by engineering reporter proteins such as the firefly Luciferase, the Renilla luciferase, the Infrared fluorescent proteins, and even the superfolded GFP. We split the reporter proteins and fused them to an E.Coli endogenous protein involved in the regulation of extracytoplasmic stress. The protein of interest is CpxR, a component of the CpxA-CpxR two-component regulatory system.

On top of developing the biological components allowing fast response to stimuli, we engineered a small, cheap and easy to use “microscope” mainly made of a small camera to detect the position of the emitted light, process the information and instruct the associated electronic device that the user is touching the BioPad a given position.

The CpxA-R Pathway

The natural function of the CpxA­-CpxR two component regulatory system in bacteria is to control the expression of ‘survival’ genes whose products act in the periplasm to maintain membrane integrity. This ensures continued bacterial growth even in environments with harmful extracytoplasmic stresses. The CpxA­CpxR two component regulatory system belongs to the class I histidine kinases and includes three main proteins:

  • CpxA -­ an integral inner­membrane sensor kinase, which activates and auto­phosphorylates when sensing misfolded proteins in the E.Coli periplasm. CpxA transduces its signal through the membrane to activate the cytoplasmic CpxR response regulator by a phosphotransfer reaction.


  • CpxR ­- CpxA’s corresponding cytoplasmic response regulator belongs to the OmpR/PhoB family of winged­helix­turn­helix transcriptional response regulators and is phosphorylated by CpxA in the presence of extracytoplasmic stresses. Phosphorylation induces CpxR’s homo­dimerization, and activation as a transcription factor. Phosphorylated CpxR then binds to the promoters of genes coding for several protein folding and degradation factors that operate in the periplasm.


  • CpxP -­ an inhibitor of CpxA that we suspect to actively compete with misfolded proteins (CpxP is a chaperone).

Engineering: CpxR and split complementation techniques

The main component that we wish to engineer is CpxR. It has been reported that the protein homo-dimerizes upon activation. We thus plan to use fused split proteins of fluorescent and bioluminescent nature to detect its activation.

As a preliminary step, we used two fluorescent proteins sfGFP and IFP to characterisation CpxR. Split sfGFP (superfolded GFP) is an irreversible split system which will be used to prove the dimerization of CpxR. Split IFP on the other hand (Infrared Fluorescent Protein) is a reversible split system which will be used to understand the spatio-temporal dimerization of CpxR and thus allow us to better understand the On/Off mechanism of this system.

To achieve our final goal, we will engineer split bioluminescent proteins: Firefly and Renilla split Luciferases. These constructs will be the main component of our system. When fused to CpxR, we are expecting to witness emission upon touch.

Engineering: Microfluidic chip interface

Our specially designed microfluidic chip, hereafter known as BioPad Chip, will allow easy and accurate induction of fluorescent or bioluminescent signals. The chip is made up of thousands of compartments – representing the pixels of our device ­ of the height of a bacteria. The BioTouch Chip thus allows the effective trapping and induction of stress onto our engineered bacteria.

Engineering: The BioPad Detector

The signals induced by the BioTouch Chip are then processed by our self designed detection system: the BioTouch Detector. The BioTouch Detector is mainly made of a cheap computer (Raspberry Pi), a highly sensitive digital camera with appropriate light filters, and a light emitting source. The BioTouch Detector locates signals from various sources (infrared fluorescence, green fluorescence and luminescence), processes them and sends back the relative positions of the signals with respect to the BioTouch Pad. Thanks to this position, we are able to tell extract information such as giving a computer operating system that the position represents the position of the mouse on a screen, that the well at the given position is a suitable antibiotic candidate, or that a gene of interest has been activated. We therefore effectively control a computer or any other electronic device through a living interface: the BioTouch Pad.

Touch Pad

Our Touch Pad will be the first biological track pad. The pad itself will need nothing else than a little water and nutriments to be operational. The EPFL Bio touch pad aims to be a proof of concept for the introduction of biological components in engineering. As such, futuristic applications of this technology include a substitute to “traditional” touch pads. This could have an economic and ecological impact as indium oxide, the main component of today’s touch screens, is being rapidly depleted (some estimate depletion by 2030).

Drug Screening

One of the applications of the EPFL Bio Touch pad is drug screening. This is because it could allow researchers to track the activation of certain pathways by luminescence. Thanks to our light detection and localization system, researchers could screen small molecule libraries in a fast, fully automated, and cheap way. We could apply this concept to find molecules that could affect the biological pathway used for our Bio Pad project.

Touch Pad

Our Touch Pad will be the first biological track pad. The pad itself will need nothing else than a little water and nutriments to be operational. The EPFL Bio touch pad aims to be a proof of concept for the introduction of biological components in engineering. As such, futuristic applications of this technology include a substitute to “traditional” touch pads. This could have an economic and ecological impact as indium oxide, the main component of today’s touch screens, is being rapidly depleted (some estimate depletion by 2030).

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